Yeah Sr only finds out what happened to his son after he becomes director in Peacemaker. But it's pretty much "now that I'm director, give me my son's files." Maybe going against Waller in commandos gave him a new perspective, or maybe in commandos he was putting on a show the whole time just to become director and find out.

Either way, everyone keeps telling him it was Waller not Peacemaker, but Sr just seems blind obsessive with zero care about anything else but revenge whereas he seemed more mentally grounded to me in commandos.